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I am currently using Linux Mint 7 x64, though this issue is also present in Linux Mint 6 x86 and Linux Mint 7 x86. I have tested this issue on multiple computers, including VirtualBox installations of Linux Mint 7 x64 and x86.

I keep my main Mint panel docked at the top of my screen with it set to auto-hide. I also created a new panel and docked it at the bottom of my screen (I use it sort of as a "quick launch" panel). If I keep it expanded, everything works just fine. However, if I uncheck the "Expand" checkbox in the properties for the bottom panel, it will appear at the top of my screen when I reboot.

I have tested this by docking the "quick launch" panel at the left side of the screen, and it stays where it is supposed to upon restart. However, any time I keep it docked at the bottom, with "Expand" disabled, it always repositions itself at the top of the screen on restart.

Does anyone know how to solve this issue? Is this a bug? Does anyone know if this is present in Ubuntu (I doubt it, since Ubuntu generally places the main panel at the top of the screen, rather than the bottom - as is the default in Mint)?

I agree, but you may want to be careful with that observation. In gconf, -1 also often means "last used" (case in point: mintMenu). When editing gconf, just try to be careful what you are changing from and changing to.